GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Rhodobacter viridis JA737

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  342 bits (877), Expect = 2e-98
 Identities = 186/481 (38%), Positives = 287/481 (59%), Gaps = 11/481 (2%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L  +G VK +PG  A+  VDF++    +  L+GENGAGKSTL+K++ GV     G I ++
Sbjct: 9   LSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTITMD 68

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           G  + F +  DA   GI ++ QELNL  N++VAENIF+ +E  RG        +D     
Sbjct: 69  GREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHETTRG-----GIDIDIEAHR 123

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
             +++L++ +     PD  + NL   Q+Q+VEI KAL +  RI+ +DEPTS+L+  E E 
Sbjct: 124 EATRQLMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEV 183

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
           LF +I+ L ++G+ +V++SHRL+E++R+ D I V+RDG   G       D+  I+K M+G
Sbjct: 184 LFRVIDELTAQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPWIVKAMIG 243

Query: 255 REVEFFPHGIETRPGEIALEVRNLKWKDK-----VKNVSFEVRKGEVLGFAGLVGAGRTE 309
              + +        G       ++          V +VS  +R GE++G  GL+GAGR+E
Sbjct: 244 SSSKEYGRSEVANFGPEIFRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRSE 303

Query: 310 TMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369
            +  V   +    G  +V G+ +  ++    I  GI LIPEDRK  GL+  M++++N+ L
Sbjct: 304 FLECVMAQHPHSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLTL 363

Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429
            SL   ++    LD +KE + + +++KRL+IK  S      +LSGGNQQKVV+ K L T 
Sbjct: 364 SSLPSFTKL-FHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKALMTG 422

Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489
             +L+ DEP+RGID+GAKAE+ R +R LAA+G  ++ ++S+L E+L LSDRI+VM +G +
Sbjct: 423 PKVLLMDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRV 482

Query: 490 T 490
           T
Sbjct: 483 T 483



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 66/233 (28%), Positives = 113/233 (48%), Gaps = 7/233 (3%)

Query: 13  EILKAKGI-VKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEI 71
           EI +A+ I + R  G   VD+V   +   EIV L G  GAG+S  ++ +        G+ 
Sbjct: 260 EIFRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLECVMAQHPHSGGKF 319

Query: 72  LVNGERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRV 128
            V G+ +          +GI++I ++     L   M++ EN+ L+      +   L  + 
Sbjct: 320 WVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLTLSSLPSFTKLFHLDLKK 379

Query: 129 DENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188
           +        K L   +    SP+  V +L+   +Q V I KAL+  P+++ MDEP+  + 
Sbjct: 380 EAKTAVEFIKRLTIKVA---SPENPVSSLSGGNQQKVVIGKALMTGPKVLLMDEPSRGID 436

Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKG 241
           +     +F  +  L + G+ ++FV+  LDEV+ +SDRI+VM  G+  GE   G
Sbjct: 437 IGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRVTGEFPSG 489


Lambda     K      H
   0.319    0.138    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 662
Number of extensions: 27
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 520
Length of database: 511
Length adjustment: 35
Effective length of query: 485
Effective length of database: 476
Effective search space:   230860
Effective search space used:   230860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory